Hi Mark,

As I wrote in my previous post, there are so many repetitive elements (vaults, wall sections etc) in your model that the use of components would really enhance your modeling workflow. Then you could put them on different layers and only work with the parts shown while keeping the rest of the model hidden.

Another thing is that you have quite a lot of back (blue) faces in the model - these should be reversed (select a bunch of them, then right click any of them and select "reverse faces" from the context menu).

I think that to work "inside" the building, you could use section planes successfully.